Mass Effect 4: A Matter of Control
by Gelious
Summary: Mass Relays were destroyed,Reapers left the Earth with no apparent reason and Commander Shepard disappeared. Admiral Hackett and his allies are trying to understand what happened and what to do now, when Shepard returns with shocking news...
1. Prologue: The Choice

**Autor Note: This is my version of how exactly Mass Effect 3 ended and what should happen next. I don't own anything, Bioware does.**

Mass Effect 4: A Matter of Control.

Prologue: The Choice.

_I never wanted any of this._

And yet here he was, Commander John Shepard, first human Spectre, standing at the top of the Citadel, presented with three options, each of them changing the galaxy in the ways most unpredictable and unimaginable.

_I never wanted to be responsible for the future of my own people, not to mention the whole friggin galaxy. All I ever wanted is to serve humanity, the Alliance, and – as a Spectre – the Council and all races. But not like this!_

But now Shepard himself had no choice. He was tired. More than anytime before, more that he thought it was humanly possible. Even worse, Shepard was dying. And out there, on the Earth and above it, his friends and allies were fighting. And dying too.

_Fine. Lets get it over with._

For the last time Shepard looked at the Catalyst, but the boy was silent and clearly watching the battle that took place on the Earth's orbit.

_He won't help me. He gave me a choice and now is waiting for the result and there is nothing I can do about it. So much for my small talk with the Iillusive Man. Stupid machine._

Shepard sighed and turned back to the beam of light, trying to clear his thoughts, ignoring the pain that threatened to consume his body.

_So what are my options here again?_

First, destroy Reapers. Normally this two words alone would be enough for Commander's to make a choice here and now, but… It wasn't about just destroying Reapers. The Catalyst said that the Crucible will wipe out all synthetic life forms, including geth. Including EDI, though this fact was never mentioned.

_Hell, even Quarians can die if their suits will stop working before they will be able to adapt to the environment of their lost homeworld, Rannoch. Not to mention me, with all the tech Cerberus put in me._

But the real question was… could he do it? Could Shepard betray the geth, who kept all their promises and followed him into the battle for his own homeworld? Could he destroy the uneasy alliance between synthetic and organics that Commander himself helped to create in spite of everything the Catalyst said? Was Shepard willing to commit genocide of his own only to escape another one? Was it even worth it?

He slowly realized that the answer was "No."

_I am sorry… I can't do this. If to save my people I must destroy another species, If to stop the genocide I must commit one… then me and all living creatures are no better then the Reapers. The cost of survival is high, I know this better than anyone, but this is wrong. I must find another way._

Shepard sighed again and looked into the beam of light that was ahead.

Convergence… could this be the answer? Bringing a new combined form of life into the galaxy, thus ending the Reaper's cycle and destroying the very reason for their actions, ensuring peace… Yes, that could be the perfect solution.

Shepard started to slowly walk towards the light, then his pace became quicker. Commander even started to run… only to froze in place when a new thought occurred to him.

_The galaxy never asked for it. Asari, turians,_ _salarians, humans… they didn't ask to be turned into some kind of hybrid creatures. They were not given a choice. Only Reapers want this to happen, just like they want to harvest all advanced life_. _The boy said it all is a part of the same cycle… but here is the thing – I don't believe in any of this crap, just like I don't believe that synthetics is bound to destroy organics. I always stood for the free will and the ability for everyone to choose their own future. If we are truly destined to achieve unity with synthetics because of natural evolution, we will do it by ourself, not because some genocidal AI and it's unstoppable fleet are telling us to do so. Who was the first to come up with this idea anyway? Don't know and don't care. They can all go to hell, I am not going to do their dirty work for them. I am not going to enforce the Reaper's will on the galaxy. _

But that left the Commander with no choice other then…

The whole Citadel suddenly and violently shook.

"You time is almost up", - calmly said the Catalyst, - "Reapers are attacking the Crucible. When it will be destroyed, the cycle will continue as before. And you will die".

Shepard didn't answer. His mind was processing the last option left for him.

_Can I really do this? Control the Reapers? I will be able to stop the war. Furthermore, I can use the knowledge, stored inside them to help rebuild the mass relays. And recreate all that the Reapers already destroyed – Earth, Palaven, Thessia and many more…_ _With me controlling them there will be no next cycle of_ _galactic_ _extinction , nor will I let anyone to start another devastating war. _

He suddenly remembered Garrus's words: "You are a peacemaker, Shepard. A rare thing these days. Now, if you can pacify the Reapers, we'll make you a saint."

_I never wanted to become a saint, but if for the galaxy to know eternal peace , I must forever keep the Reapers at bay… so be it!_

Shepard recalled other words as well, and they were not so pleasant: "You will die. You will lose everything " , but he didn't care anymore.

_I will die anyway, and others will soon follow. I have to stop this. illusive Man wanted to gain control over the Reapers for the benefit of the mankind alone and failed, because he allowed them to get to him first. Now I have a chance to do the same, but I will use the Reapers for benefit of every race. _

Commander gathered his last strength and run to the left, to two long cylinders, which were seething with energy. Shepard placed his hands on both of them.

_Is this what supposed to turn me into some Reaper Overlord? How does it work exactly?_

The unknown device started to produce massive waves of blue energy, which engulfed and eventually consumed Shepard's body, until it simply disappeared as if it never existed .

While he was changing, Shepard felt nothing, only cold and numbness, and before darkness took him, Commander's last thought was:

_I am sorry, Liara, but I couldn't keep my promise._


	2. Chapter I:  Repercussions

Chapter I.

Repercussions.

The Sword Fleet wasn't doing very well.

Admiral Hackett was currently aboard his flagship SSV Orizaba, bent over holographic map of the Sol system, coordinating the allied fleets of all races, trying to concentrate their fire on single targets, namely Destroyers and Capital Ships of the Reapers. His efforts was successful to a certain degree - Sword Fleet already destroyed about a dozen Destroyers and even managed to cripple a few Capital Ships.

But those minor victories came with a great cost. While it took a massive firepower of a large number of ships to overcome Reaper's vessel defenses and to do enough damage to tear apart it's hull, it took only one, in the best case a few strikes of Reaper's red beam to completely destroy any ship in the Sword Fleet, except maybe the Destiny Ascension, but even asari were taking heavy casualties.

Even worse, Reapers' losses were too small compared to overall number of their forces in the Sol system to have any positive impact on the battle. And already reports were coming, indicating that new enemy ships are entering the system, seemingly from nowhere, not even using the Charon Relay.

Apparently Reapers decided to accelerate the destruction of the resistance.

_It's a good thing we never planned to win this battle on our own, then._

The whole fight, both in space and on the Earth's surface was merely a distraction, an attempt to give Commander Shepard enough time to reach the Citadel and activate the Crucible, which was supposed to destroy all Reapers or at least make them vulnerable enough to be defeated via conventional means. Unfortunately, it was also the part, where something went very wrong.

Commander John Shepard was last seen on the ground, participating in charge towards the beacon, which was the only way to the captured Citadel, when his forces came under attack from a few Capital Ships of the Reapers, including Harbinger. As a result of the attack everyone around Shepard was considered dead or went missing, with the exception of former turian C-Sec officer Garrus Vakarian and asari scientist Liara T'soni. Both of them were picked up by the shuttle, piloted by Lieutenant Steve Cortez_, _and safely returned to Normandy, although they failed to inform Hackett of Shepard's possible whereabouts. However, both of Shepard's friends expressed a strong belief that Commander is indeed still alive and has successfully reached the Citadel. Naturally, they had no real proof to back up their claim.

Roughly forty minutes later Hackett got all the proof he needed, when Admiral heard Shepard's voice on the comm. Commander sounded tired, unsure and exhausted. Shepard must have suffered severe injuries and his last words weren't very reassuring either. He opened the Citadel's arms, but Hackett still needed Commander to activate the damned Crucible, despite the fact that neither of them had any idea how to do it.

Another thirty minutes passed. Hackett tried to raise Shepard on comm for a dozen times, but received no answer. A terrible picture sprang in his head – Shepard, lying in a pool of his own blood only a few steps away from the button, that must put an end to the nightmare called Reapers.

_No! He wouldn't do this to us. Shepard didn't surrender on Akuze, and he sure as hell wouldn't abandon us now. Come on, Commander! Don't you dare to die without getting the job done!_

The worst thing was, Admiral couldn't even send anyone to help Shepard or replace him. Harbinger and his lackeys continued to guard the beam on the ground, while the whole swarm of Oculuses was patrolling the space near the Citadel, supported by a few Destroyers and a Capital Ship. All vessels which tried to enter the structure ended up destroyed. Meanwhile Normandy was trying to get inside since Vakarian and T'Soni were taken aboard, but succeed only in staying in one piece. Hackett already tried a few times to order Flight Lieutenant Jeff Moreau to leave the Citadel alone and join the fight, to which Joker irritably advised Admiral to stop pretending that this fight was more important then Shepard's mission inside the Citadel. Hackett was not very happy with Moreau's ignoring his direct orders, but Admiral was too busy coordinating the rest of the Sword Fleet to insist. Besides, Lieutenant Moreau hold the fame of the best pilot in the Alliance, so perhaps he indeed had the biggest chance of getting inside the Citadel.

_Which still doesn't change the fact that no one knows, how to activate the Crucible._

Suddenly Hackett's unhappy thoughts were disrupted by the voice of Hannah Saint, captain of the SSV Orizaba:

"Admiral, look!"

Hackett traced her gesture to one of the control screens nearby, which was monitoring the Citadel, and froze, when he saw a large sphere of light blue energy, emerging from the opened Citadel. The ball continued to rapidly grow in size, as if it wanted to contain the entire Sol system inside itself.

And before Hackett had time to order his ships to stay the hell way from this blue energy just in case, Admiral saw it went through the ones closest to the Citadel without doing them any visible harm. Second later various captains reported that their ships didn't register any damage, and the crew felt nothing either.

_Thank God Crucible doesn't seem to affect non-Reaper forces. But what about the Reapers themselves?_

Hackett got the answer soon enough, since there were a lot of Reapers' ships in close proximity of the Citadel. The blue energy went through them without any visible effect… save for the fact, that their insides now were shining with light blue instead of bright red.

_I have no idea what this supposed to mean, but it can be our only chance for victory._

"To all ships of the Sword Fleet", - commanded Hackett,- "concentrate your fire on Reapers, affected by this energy, whatever it is."

They did as was told, but nothing really happened. Reapers' ships took a certain amount of damage, but it was no different than in their usual state. Whatever the Crucible did to enemy vessels, it clearly didn't affect their defenses.

Before Admiral could think about anything else, another report came:

"Admiral", - said Captain Saint, - "our sensors have just detected a large exhaust of eezo in the location of the Charon Rela…" And then she suddenly shouted: " Admiral!"

Hackett once again turned to the control monitors, one of which was now showing the Charon Relay, just in time to see it exploding when the part of now enormous light blue sphere reached it.

_Oh. My. God._

Hackett felt his heart stopped beating… or so he thought. What did it matter anyway? Now, when he and his whole fleet were stranded here, unable to retreat or to get reinforcements (which didn't exist in any case), when the homeland of the humanity was cut off from the galactic community and was at mercy of Reapers… and they will have none.

_It's like we were locked up in the cage with a hungry lion and the key was immediately thrown away. Damn you, Shepard, what have you done__?_

But before Hackett could issue any further orders (not that he had any in particular except "everyone, fight to the death"), he heard the voice of Captain Saint again:

"Admiral, we are receiving multiple reports, that all indicate the same thing",- said she, -"Sir, Reapers have stopped fighting our forces. Their ships are seen leaving the Earth".

"What?" – snapped Hackett, losing his calm tone for the first time since the battle of Earth started,- "Captain, repeat!"

"I repeat, all Reapers' vessels have stopped firing at us and are moving towards the location… former location of the Charon Relay", - obediently answered Hannah Saint, - "Our troops report that enemy ground forces have either collapsed or exploded or simply stopped performing any action whatsoever… Admiral, what's going on?"

Hackett looked at her, but didn't answer. Not aloud, anyway.

_I wish I knew, god dammit._

"All allied forces of the Sword Fleet", -he said at last, - "Do not pursue the Reapers, I repeat, leave them alone. Gather all ships around the Citadel and assume defense position. All ground troops, take out all husks in your immediate vicinity and wait for further orders. SSV Normandy prepare to…"

Admiral stopped, when he realized that Normandy has disappeared from all control screens and the Orizaba's scanners can't find it anywhere. Granted, it was a stealth ship after all…

"SSV Normandy, this is Admiral Hackett, do you copy, over? Lieutenant Moreau, do you hear me, over?"

No answer came. Soon other ships confirmed that they couldn't detect Normandy and never had any contact with the ship.

Normandy was near the Citadel when the Crucible fired. Now it vanished, just like the Reapers' fleet disappeared somewhere behind Pluto. And the sphere of blue energy was gone too, but not before it engulfed the Earth.

_But Crucible did nothing to the planet or to our ships._

Hackett sighed. The fact that Crucible didn't perform as expected was bad enough, now they lost both Commander Shepard and his ship. And the the Charon Relay was gone, meaning that no one of their allies will be able to return home anytime soon, and the Earth has to recover on its own.

_If it will have any time to recover at all. Where did all the Reapers go anyway and for how long_?

The possibility that the Charon Relay wasn't the only one that got destroyed haven't crossed Admiral's mind yet. But the current situation looked pretty grim to him and right now Hackett had no idea how new inhabitants of the Sol system are going to live through it.

**Author note**: Just like a lot of other people I didn't really like ME 3 endings. But instead of trying to replace them, I decided to roll with the one, I thought the best and bring it to a closure (maybe even a happy one). It is the Control Ending, as you see.

**Sith Lord Darth Revan** - It will not be focused on Liara and Shepard relationship. Liara will have an appearance, assuming I ever get that far, but I am far more worried about the fate of the galaxy and Shepard's role in it, than the romance. Sorry, shippers. I like Liara though.

**calilove, DestinyDragon01** - Actually it was supposed to be a story, not a one/twoparter. I am just afraid I am not good enough as a writer to finish it properly. I see how things will unfold in my head, vaguely, but it make sense to me. But I fear my writing skills and my imagination could be not enough to make it clear and understandable for everyone else. I don't want to write bad, I better won't write at all.


	3. Chapter II: Inside

Chapter II.

Inside.

In the beginning there was only darkness, deep and endless like the space itself, but devoid of all stars. Dark space…

But there was something else too. A human male, standing in the middle of the place, that is, if the never ending darkness could have a center.

His body suddenly jerked and his blue eyes opened wide, as the man's memory started to return to him.

He remembered now, that he was Commander John Shepard once….

… who was born on Earth and nearly died on Akuze….

… who stopped Sovereign and saved The Citadel _Council…_

… who waged war against the Collectors with the help of the organization called Cerberus and won, destroying Collectors' base in process…

… and who died, trying to take control over the Reapers, although he had no idea how to do it.

Or did he?

_Where the hell I am? Can't see a damn thing…_

Suddenly darkness around Shepard began to change. Middle-sized screens in red frame started to appear all around him, not only in front of the Commander or at his sides, but even above his head and beneath his feet. All of them were showing him something, and every moving picture was different.

Surprised and curios, Shepard looked at many screens and although the images on them were different, they all had something similar: living beings (mostly asari, turians, salarians, humans and krogans ) shouting, screaming, shooting and dying, different starships producing flashes of energy and blowing up, many buildings and even planets on fire….

Most of the places shown on those screens were completely unfamiliar to Shepard, but as he looked from one monitor to other, Commander, to his horror, started to notice a few familiar sights…

Cold rocks of Palaven's moon. Burning ruins of Thessia's temples. Damaged tower of Big Ben.

Then it dawned on him – a simple, yet shocking truth.

"_I now see the whole galaxy through the eyes of the Reapers… but I can't hear anything. Why__?_"

Almost immediately Shepard fell on his knees and pressed his hands against his ears, trying to protect them from an overwhelming wave of sounds, that suddenly hit him. Sounds of screams, explosions and weapons firing threatened to overload Shepard's brain and destroy his consciousness. Without thinking, Commander shouted:

"Stop it!"

Only no sound escaped Shepard's lips. What he thought about as a scream, came out as a silent thought, that only felt like he actually shouted it.

Nevertheless, all sounds disappeared, although the screens and the images on them remained. Shepard slowly removed his hands and stood up. Now he began to understand.

_Whatever this place is, it reacts to my thoughts, as if they are actual commands. Lets see if I can use it to influence the Reapers._

He tried to concentrate and then formed a thought:

_To all Reapers' ships I command you to stop all your fighting immediately and retreat beyond the edges of the star system, in which you are currently in. All ground troops are to stand down and deactivate themselves._

Honestly speaking, Shepard had no idea, if it is even possible for all those husks to be deactivated. They were not geth after all… But he had to stop them, somehow and couldn't waste time to order them to return aboard Reapers' ships. Not to mention that the very thought of having all this creatures who once were sentient beings, and then were transformed into monsters against their own will, under his command was terrible.

_Maybe there is still a way to help them or at least to end their existence quickly…_

For a few long seconds nothing happened. Then the images on the screens began to change slowly. Some of them produced a bright white flash, went dark, and then disappeared in darkness only to be instantly replaced by some other screen. But on most monitors the picture remained, however, it no longer showed ruins of different buildings or ships of various races. Instead on some screens Shepard saw the atmosphere… and then all of them were showing only open space.

_I did it! Their ships are retreating! Those disappeared screens probably were husks who were disabled…_

"**Good job for a primitive organic being, Shepard."**

It wasn't an actual voice. Once again, it felt more like a thought, but it had a tone, and the tone sounded very familiar…

"Harbinger?" - asked/thought Shepard.

"**Indeed", - **came the thought/the reply, -** "Or did you expect to enter our Network without me noticing, human?"**

"Your network? You mean like the one the geth ha… "

"**No." – **there was a clear hint of annoyance in Harbinger's thought,- "**The geth are – or should** **I say were, since you gave them our code- a primitive, basic form of an AI. Unlike them, we do not need our Network to maintain actual intelligence. Each of us is a highly intelligent** **AI by itself, which consists of thousands of intelligent programs.**"

"Then your Network is basically…"

"**Yes**", - Harbinger finished Shepard's thought, - "**It is a way of communication between our AIs and a way to send orders to lesser minds. To primitive beings, it can be described as a telepathy.. or connections via Quantum Entanglement Communicators. Doesn't matter, which you choose, since it is poor analogy to begin with.** "

"So… ", - Shepard couldn't help but ask, - " was Sovereign a part of this Network too? "

"**Of course he was, Shepard. The Network transcends space, reaching every corner of the galaxy. Even dark space. "**

"And still I defeated him**", - ** pointed out Commander, -"Your precious Network didn't help him, did it? You Reapers are not so advanced as you want everyone to think… or maybe it's **we** who are not so primitive as you **like** to think. "

"**Your petty speculations are empty and pointless, Shepard. Nazara died only because in the end, he became too arrogant. Your so-called superiority had nothing to do with it."**

"Care to explain?**"- **demanded Shepard.

"**Isn't it clear for you already, Shepard? Nazara chose to ignore the fact that the time is always on our side. Instead of wiping the rest of your pathetic fleet first, securing the space around the Citadel and then sending all geth ground forces with Saren to the console, Nazara decided to ignore your ships outside the Citadel and accelerate the process by rushing to it's control room. You are aware of the result. Would Nazara had done as I suggested you would have faced Saren and legions of his geth and the cycle would have begun much earlier."**

"Any ideas why Nazara didn't listen to you?**"**

"**He was too proud of himself to listen to others. Nazara always thought that organics are even more primitive then they really are. And when he learned that he can't activate the Citadel Relay remotely as he had done many times before, Nazara grew impatient. He fell as victim of his own mistakes, but do not presume that we are all like him. We learned from his lesson well, Shepard. "**

"Really?**"** – Commander forced himself to smile, although he wasn't even remotely happy. Shepard just needed more information about Reapers, and for some reason Harbinger was in the mood to provide him with something other, then usual "Surrender, Shepard, you can't defeat us" crap, - "What about a Human Reaper back at the Collector's base? What was his mistake exactly?"

"**Stop insulting my intelligence by pretending to be more stupid, then you already are, Shepard", - **retorted Harbinger, - **"Even for you it should have been obvious that this Reaper was merely a child by our standards. He didn't even have a connection to his inner lives, let alone our Network. No wonder you have destroyed him so easily. His construction wasn't finished. "**

"I take it by "inner lives" you actually mean programs forming his Ai…. **", - **began Shepard.

"**No!**"- now Harbinger was obviously pissed, - "**Programs are called programs, while lives are indeed lives. Although your ignorance in this question is somewhat understandable, giving your simple mind and primitive reaction to our contacts. Now tell me this, Shepard. What do you think we are doing with sentient creatures, that we take prisoners and do not turn into husks? **"

''I saw what you are doing with them", - reminded him Shepard, - " Those colonists at the Collectors' base…. you melted their bodies and then pumped them into your new Reaper"

"**Exactly, Shepard**", - Harbinger seemed to be completely satisfied by Commander's answer, - "**But do you know what happened with those beings next?**"

"Nothing", - said Shepard, - "Because they were dead. Their remains became some part of your inner systems"

"**Wrong, Shepard. Those who are absorbed inside us are not dead. Nor do they become any part of our system… not in the way your primitive brain sees it anyway. Their minds still exist , surrounded and protected by countless programs of our AI. This is why we call the process of converting organic beings ascension. But when we die, our inner lives die with us. Therefore, by killing our so-called Human Reaper, you, Shepard, also ended lives of all the colonists that the Collectors found for us. Now tell me, human, does it still sounds like a victory to you? "**

* * *

><p><strong>Author Note: Sorry for the delay, but I just had to read two new books "Fate of the Jedi: Apocalypse" and "Mass Effect: Deception" The former was okey, the latter was terrible. I am also preparing for exams and making a second ME 3 run with my FemShep, so don't expect daily updates. Sorry.<strong>

**P.S. This is the first chapter that is not based on what I already saw in ME 3 ending but rather came entirely from my head. Hope it's not bad :)  
><strong>


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